Hey Zeus, I keep my tracks organised into playlists on my HDD - each playlist has its own folder. So when I buy new tracks I sort them into their respective playlist folder on my HDD and make a note of which folders I've updated with new tracks. Then in rekordbox I select the playlist I want to update and drag and drop the entire folder contents into the playlist. Rekordbox identifies duplicate tracks and asks if you want to skip them... when you click 'skip' it only imports the new tracks. I find it really easy to manage everything this way. I rarely even look at the collection pane any more unless I want to search my whole collection for a track during a set.
I also use Traktor and follow a similar process with that software.